recipe pblat

blat with multi-threads support

Homepage:

https://icebert.github.io/pblat

Developer docs:

https://github.com/icebert/pblat

License:

OTHER

Recipe:

/pblat/meta.yaml

Links:

biotools: pblat, doi: 10.1186/s12859-019-2597-8

package pblat

versions:

2.5.1-2,  2.5.1-1,  2.5.1-0,  2.5-2,  2.5-1,  2.5-0,  2.4-0,  2.3-0

depends libgcc-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends openssl:

>=3.1.0,<4.0a0

depends zlib:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install pblat

and update with::

   mamba update pblat

To create a new environment, run:

mamba create --name myenvname pblat

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/pblat:<tag>

(see `pblat/tags`_ for valid values for ``<tag>``)

Notes

pblat is modified from blat, the licence is the same as blat. The source code and executables are freely available for academic, nonprofit and personal use. Commercial licensing information is available on the Kent Informatics website. To cite: Wang M & Kong L. pblat: a multithread blat algorithm speeding up aligning sequences to genomes. BMC Bioinformatics 2019, 20(1).

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